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Each Alignment has:
Each Alignment has:
* query name, QNAME (SAM)/read_name (BAM). It is used to group/identify alignments that are together, like paired alignments or a read that appears in multiple alignments.
* query name, QNAME (SAM)/read_name (BAM). It is used to group/identify alignments that are together, like paired alignments or a read that appears in multiple alignments.
* a bitwise set of information describing the alignment, FLAG:
* a bitwise set of information describing the alignment, FLAG. Provides the following information:
** are there multiple fragments
** are there multiple fragments?
** are all fragments properly aligned?
** is this fragment unmapped?
** is the next fragment unmapped?
** is this query the reverse strand?
** is the next fragment the reverse strand?
** is this the 1st fragment?
** is this the last fragment?
** is this a secondary alignment?
** did this read fail quality controls?
** is this read a PCR or optical duplicate?
Not all alignments contain The rest of the alignment fields may be set to default values if the information is unknown.
Not all alignments contain The rest of the alignment fields may be set to default values if the information is unknown.
* leftmost position of where this alignment maps to the reference, POS. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. Beware to always use the correct base when referencing positions.
* leftmost position of where this alignment maps to the reference, POS. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. Beware to always use the correct base when referencing positions.
* mapping quality, MAPQ, which contains the "phred-scaled posterior probability that the mapping position" is wrong. (from SAM-1.pdf)
* mapping quality, MAPQ, which contains the "phred-scaled posterior probability that the mapping position" is wrong. (from SAM-1.pdf)
* CIGAR
* string indicating alignment information that allows the storing of clipped, CIGAR
* the reference sequence name of the next alignment in this group, MRNM or RNEXT. In paired alignments, it is the mate's reference sequence name. (A group is alignments with the same query name.)
* the reference sequence name of the next alignment in this group, MRNM or RNEXT. In paired alignments, it is the mate's reference sequence name. (A group is alignments with the same query name.)
* leftmost position of where the next alignment in this group maps to the reference, MPOS or PNEXT. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. Beware to always use the correct base when referencing positions.
* leftmost position of where the next alignment in this group maps to the reference, MPOS or PNEXT. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. Beware to always use the correct base when referencing positions.
